update to use new env files

Dockerfile

@@ -4,75 +4,24 @@ FROM continuumio/anaconda3
 # Set environment variable to avoid user interaction during package installation
 ENV DEBIAN_FRONTEND=noninteractive
 
-## Update package list and install necessary packages for X11, Qt, and basic utilities
-#RUN apt-get update && \
-#    apt-get install -y \
-#    x11-apps \
-#    xauth \
-#    libx11-dev \
-#    libxext6 \
-#    libxrender1 \
-#    libxrandr2 \
-#    libxfixes3 \
-#    libxi6 \
-#    libxkbcommon-x11-0 \
-#    libgl1-mesa-glx \
-#    libqt5widgets5 \
-#    libqt5gui5 \
-#    libqt5core5a \
-#    fonts-dejavu-core \
-#    pciutils \
-#    make \ 
-#    less \
-#    nano \
-#    && apt-get clean && \
-#    rm -rf /var/lib/apt/lists/*
-
+# Update current packages and install some useful tools. libgl1-mesa-glx necessary for spyder
 RUN apt-get update && \
     apt-get install -y \
-    libgl1-mesa-glx \ 
+    libgl1-mesa-glx \
     less \
     nano \
     && apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-RUN useradd -ms /bin/bash clarkad 
-
-# Set environment variables for X11 forwarding and Qt plugins
-#ENV DISPLAY=:0
-#ENV QT_QPA_PLATFORM=xcb
-#ENV QT_PLUGIN_PATH=/usr/lib/x86_64-linux-gnu/qt5/plugins
-
-RUN conda create -y -c conda-forge -n spyder-env spyder numpy scipy pandas matplotlib sympy cython
-
-# Ensure conda is initialized in every new shell
-#RUN echo "source /opt/conda/etc/profile.d/conda.sh" >> /opt/.bashrc
-#RUN echo "conda activate spyder-env" >> /opt/.bashrc
-
-##----------------------------------------------------------------------------##
-## Install parallel
-##----------------------------------------------------------------------------##
-
-#WORKDIR /opt
-#COPY ./parallel.tar.bz2 /opt
-#RUN tar -xjf parallel.tar.bz2
-#
-#WORKDIR /opt/parallel-20240322
-## build and install
-#RUN ./configure && make && make install
-#
-#WORKDIR /opt
-## verify version of parallel installed
-#RUN parallel --version | head -1
-## get past annoying parallel citation prompt
-#RUN echo 'will cite' | parallel --citation &> /dev/null || true
+RUN useradd -ms /bin/bash clarkad
 
-#COPY ./cellxgene.txt /opt
-#RUN conda create -n cellxgene --file /opt/cellxgene.txt
-#RUN echo "conda activate cellxgene" >> /opt/.bashrc
+# Create the spyder environment to run out of. The container will start with this environment active, but you can switch to a different kernel inside spyder and have it run without issue
+ADD spyder_env.yml /tmp/spyder_env.yml
+RUN conda env create -y /tmp/spyder_env.yml
 
-ADD cxg_env.yml /tmp/cxg_env.yml
-RUN conda env create -y -f /tmp/cxg_env.yml
+# Create the cellxgene environment based on an environment file. 
+ADD cellxgene.txt /tmp/cellxgene.txt
+RUN conda env create -y -n cellxgene -f /tmp/cellxgene.txt
 
 SHELL ["bash"]
 ENTRYPOINT [ "conda", "run", "--no-capture-output", "-n", "spyder-env", "spyder" ]
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